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ALBUQUERQUE, N.M. — Nine months after he was branded a threat to national security and put in solitary confinement, Wen Ho Lee was set free Wednesday with an apology from a judge who said the government’s actions “embarrassed our entire nation.”

Supporters cheered as a smiling Lee left the courthouse alongside his family. He thanked them and said, “I’m very happy to go home with my wife and children today.”

With a chuckle, he added: “The next few days, I’m going fishing.”

Lee, 60, pleaded guilty to a single count of mishandling nuclear secrets as the government all but abandoned its crumbling case against the former Los Alamos scientist.

Under the terms of the plea bargain, he was sentenced to 278 days — essentially the time served since his arrest last December.

Lee had been charged with 59 counts of breaching national security and faced life in prison if convicted. Fifty-eight of those counts were dropped.

“I sincerely apologize to you, Dr. Lee, for the unfair manner in which you were held in custody by the executive branch,” U.S. District Judge James Parker said.

Parker said the Departments of Justice and Energy “have embarrassed our entire nation and each of us who is a citizen of it.”

Lee, a Taiwanese-born naturalized U.S. citizen, read a statement in court in which he admitted using an unsecure computer to download a national-defense document onto a tape. He said he knew his possession of the tape outside of the top-secret area where he worked was unauthorized.

Lee agreed to cooperate with the government and tell them everything he knows about seven missing tapes.

The government said that the fate of the tapes was paramount and that Lee’s willingness to explain what happened to them was the turning point in 2-month-old plea discussions. Lee has said the tapes were destroyed.

Federal prosecutor George Stamboulidis said Lee did not deserve a government apology. He called the downloaded information “a personal library” of nuclear defense secrets.

“Which Americans among us would want us to turn our backs on that?” he asked.

The judge said he was only sorry the plea agreement prevented disclosure of information that would have shed light on the reasons for Lee’s detention. Lee’s supporters have said he was unfairly singled out as a Chinese-American.

The judge, who was appointed by President Reagan, said he did not blame the prosecutors: “It is only the top decision-makers in the executive branch of the government, in particular the Department of Justice and the Department of Energy.”

The White House declined to comment on the judge’s criticism. “It is time to close this chapter, find out what happened to the missing tapes and move on,” spokesman Jake Siewert said.

Justice Department spokesman Myron Marlin said in Washington: “We respectfully disagree with the judge. We have an obligation to the American public to protect the national security. Before we had the assurance from Dr. Lee that he would tell us what he knows, we could not afford to do anything but detain him.”

Prosecutors also said that there are powerful incentives for Lee to cooperate.

“If at any time we believe he is not being truthful, we can seek to void the agreement and prosecute the case to the full extent of the law,” Attorney General Janet Reno said.

The investigation began as an offshoot of a Chinese espionage case, with government attorneys making dire accusations that Lee had stolen the “crown jewels” of U.S. nuclear weaponry science with the intent of handing them over to a foreign power. At the time, the government claimed the information could alter the global balance of power.